This HTML document contains the output of CATS-rf transcriptome
assembly comparison tool. For more details on each table and figure,
refer to the tool’s documentation.
Table 1. General transcriptome assembly statistics.
| Parameter | RSP_0.005_1_4 | RSP_0.01_1_4 | RSP_0.02_1_4 | RSP_0.005_5_10 | RSP_0.01_5_10 | RSP_0.02_5_10 | RSP_0.005_11_20 |
|---|---|---|---|---|---|---|---|
| N transcripts | 27748 | 30651 | 36610 | 18601 | 18652 | 19217 | 18641 |
| Total assembly length (bp) | 34167218 | 32433743 | 27462499 | 44994186 | 44145594 | 42094487 | 45586004 |
| N, % transcripts longer than 200 bp | 23903, 86.14% | 25617, 83.58% | 28233, 77.12% | 18277, 98.26% | 18225, 97.71% | 18132, 94.35% | 18371, 98.55% |
| N, % transcripts longer than 500 bp | 14553, 52.45% | 13923, 45.42% | 11423, 31.2% | 16878, 90.74% | 16738, 89.74% | 16335, 85% | 17019, 91.3% |
| N, % transcripts longer than 1000 bp | 9887, 35.63% | 8846, 28.86% | 6486, 17.72% | 13488, 72.51% | 13356, 71.61% | 12875, 67% | 13620, 73.06% |
| N, % transcripts longer than 5000 bp | 1036, 3.73% | 914, 2.98% | 608, 1.66% | 2003, 10.77% | 1931, 10.35% | 1766, 9.19% | 2024, 10.86% |
| N, % transcripts longer than 10000 bp | 93, 0.34% | 90, 0.29% | 59, 0.16% | 228, 1.23% | 221, 1.18% | 202, 1.05% | 234, 1.26% |
| N, % transcripts longer than 20000 bp | 4, 0.01% | 6, 0.02% | 6, 0.02% | 10, 0.05% | 10, 0.05% | 6, 0.03% | 10, 0.05% |
| Mean transcript length (bp) | 1231.34 | 1058.16 | 750.14 | 2418.91 | 2366.8 | 2190.48 | 2445.47 |
| Median transcript length (bp) | 547.5 | 434 | 310 | 1756 | 1714 | 1575 | 1778 |
| Transcript length IQR (bp) | 258-1570 | 234-1238 | 206-641 | 926-3168 | 899-3096 | 762-2878 | 944-3211 |
| Transcript length range (bp) | 131-60159 | 131-58349 | 131-45657 | 131-50033 | 131-50033 | 131-49970 | 131-50248 |
| N50 (bp) | 2597 | 2388 | 1831 | 3590 | 3527 | 3401 | 3602 |
| L50 | 3745 | 3737 | 3789 | 3836 | 3816 | 3748 | 3876 |
| N90 (bp) | 477 | 372 | 249 | 1215 | 1194 | 1135 | 1224 |
| L90 | 14985 | 16939 | 22581 | 12212 | 12182 | 12096 | 12283 |
| GC content (%) | 49.17% | 49.34% | 49.68% | 48.43% | 48.45% | 48.60% | 48.37% |
| % of reads mapping to the assembly | 97.71% | 96.08% | 89.99% | 99.65% | 99.53% | 98.51% | 99.67% |
| Parameter | RSP_0.01_11_20 | RSP_0.02_11_20 |
|---|---|---|
| N transcripts | 18719 | 19432 |
| Total assembly length (bp) | 45065633 | 43400943 |
| N, % transcripts longer than 200 bp | 18312, 97.83% | 18210, 93.71% |
| N, % transcripts longer than 500 bp | 16886, 90.21% | 16573, 85.29% |
| N, % transcripts longer than 1000 bp | 13517, 72.21% | 13131, 67.57% |
| N, % transcripts longer than 5000 bp | 1987, 10.61% | 1872, 9.63% |
| N, % transcripts longer than 10000 bp | 230, 1.23% | 225, 1.16% |
| N, % transcripts longer than 20000 bp | 12, 0.06% | 11, 0.06% |
| Mean transcript length (bp) | 2407.48 | 2233.48 |
| Median transcript length (bp) | 1749 | 1605 |
| Transcript length IQR (bp) | 914-3153.5 | 776.75-2950 |
| Transcript length range (bp) | 132-50317 | 132-50173 |
| N50 (bp) | 3576 | 3485 |
| L50 | 3847 | 3794 |
| N90 (bp) | 1214 | 1160 |
| L90 | 12234 | 12208 |
| GC content (%) | 48.39% | 48.52% |
| % of reads mapping to the assembly | 99.56% | 98.64% |
IQR = interquartile range
Table 2. Transcript score component statistics and assembly scores.
| Parameter | RSP_0.005_1_4 | RSP_0.01_1_4 | RSP_0.02_1_4 | RSP_0.005_5_10 | RSP_0.01_5_10 | RSP_0.02_5_10 | RSP_0.005_11_20 |
|---|---|---|---|---|---|---|---|
| Coverage score component (mean, IQR) | 0.571, 0.413-0.747 | 0.577, 0.425-0.75 | 0.586, 0.442-0.748 | 0.88, 0.839-1 | 0.883, 0.846-1 | 0.866, 0.851-1 | 0.895, 0.855-1 |
| Accuracy score component (mean, IQR) | 0.923, 0.906-0.944 | 0.882, 0.862-0.903 | 0.814, 0.785-0.837 | 0.941, 0.924-0.967 | 0.902, 0.889-0.923 | 0.781, 0.771-0.793 | 0.944, 0.924-0.972 |
| Local fidelity score component (mean, IQR) | 0.82, 0.698-1 | 0.758, 0.622-0.948 | 0.647, 0.5-0.817 | 0.969, 0.952-1 | 0.958, 0.938-1 | 0.923, 0.901-1 | 0.97, 0.956-1 |
| Integrity score component (mean, IQR) | 0.714, 0.493-1 | 0.685, 0.45-1 | 0.646, 0.408-1 | 0.92, 0.891-1 | 0.917, 0.89-1 | 0.898, 0.885-1 | 0.919, 0.888-1 |
| Assembly score | 0.349 | 0.3 | 0.219 | 0.756 | 0.719 | 0.582 | 0.771 |
| Parameter | RSP_0.01_11_20 | RSP_0.02_11_20 |
|---|---|---|
| Coverage score component (mean, IQR) | 0.895, 0.862-1 | 0.871, 0.864-1 |
| Accuracy score component (mean, IQR) | 0.908, 0.893-0.93 | 0.778, 0.768-0.79 |
| Local fidelity score component (mean, IQR) | 0.962, 0.944-1 | 0.934, 0.914-1 |
| Integrity score component (mean, IQR) | 0.916, 0.889-1 | 0.902, 0.883-1 |
| Assembly score | 0.734 | 0.588 |
IQR = interquartile range
Figure 1. Transcript score distribution.
Table 3. Coverage and accuracy statistics.
| Parameter | RSP_0.005_1_4 | RSP_0.01_1_4 | RSP_0.02_1_4 | RSP_0.005_5_10 | RSP_0.01_5_10 | RSP_0.02_5_10 | RSP_0.005_11_20 |
|---|---|---|---|---|---|---|---|
| % of covered bases per transcript (mean, IQR) | 98.63%, 100%-100% | 98.67%, 100%-100% | 98.76%, 100%-100% | 98.76%, 100%-100% | 98.79%, 100%-100% | 97.06%, 100%-100% | 98.79%, 100%-100% |
| N, % fully covered transcripts | 23038, 83.03% | 25430, 82.97% | 30104, 82.23% | 15024, 80.77% | 14980, 80.31% | 15284, 79.53% | 15099, 81% |
| N, % fully uncovered transcripts | 36, 0.13% | 42, 0.14% | 41, 0.11% | 63, 0.34% | 74, 0.4% | 409, 2.13% | 59, 0.32% |
| Mean coverage per transcript (mean, IQR) | 6.34, 3.09-7.45 | 6.32, 3.19-7.19 | 6.42, 3.32-7.37 | 33.2, 17.9-40.3 | 33.47, 17.91-40.55 | 32.59, 17.32-40.23 | 42.76, 23.51-51.87 |
| N, % bases with coverage >= 5 | 23845886, 69.79% | 23141946, 71.35% | 20451822, 74.47% | 41425701, 92.07% | 40935879, 92.73% | 39431322, 93.67% | 42562777, 93.37% |
| N, % bases with coverage >= 10 | 13358614, 39.1% | 13276215, 40.93% | 12654100, 46.08% | 37717449, 83.83% | 37394816, 84.71% | 36423117, 86.53% | 39764717, 87.23% |
| N, % bases with coverage >= 20 | 4725313, 13.83% | 4796435, 14.79% | 4864020, 17.71% | 29063963, 64.59% | 28926419, 65.53% | 28482078, 67.66% | 33564487, 73.63% |
| N, % bases with coverage >= 40 | 839997, 2.46% | 877186, 2.7% | 971977, 3.54% | 15798960, 35.11% | 15784592, 35.76% | 15709617, 37.32% | 19938620, 43.74% |
| N, % bases with coverage >= 60 | 209970, 0.61% | 208588, 0.64% | 230375, 0.84% | 9220926, 20.49% | 9260066, 20.98% | 9253720, 21.98% | 13582991, 29.8% |
| N, % bases with coverage >= 80 | 80513, 0.24% | 79379, 0.24% | 77643, 0.28% | 5744046, 12.77% | 5800514, 13.14% | 5827253, 13.84% | 8780565, 19.26% |
| N, % bases with coverage >= 100 | 35769, 0.1% | 35408, 0.11% | 33432, 0.12% | 3689834, 8.2% | 3737815, 8.47% | 3788058, 9% | 6148524, 13.49% |
| Maximum uncovered region length per transcript (bp) (mean, IQR) | 16.77, 0-0 | 14.43, 0-0 | 7.59, 0-0 | 25.71, 0-0 | 21.32, 0-0 | 19.76, 0-0 | 25.46, 0-0 |
| Mean end coverage per transcript (mean, IQR) | 1.88, 1-2.14 | 1.89, 1-2.09 | 1.86, 1-2.09 | 7.46, 2.6-10.39 | 7.54, 2.81-10.3 | 7.64, 3.03-10.37 | 9.51, 3.03-13.57 |
| N, % assembly bases in LCR | 6943649, 20.32% | 6303356, 19.43% | 4826344, 17.57% | 2680314, 5.96% | 2377600, 5.39% | 1960987, 4.66% | 2301339, 5.05% |
| % of bases in LCR per transcript (mean, IQR) | 37.1%, 10.96%-55.92% | 36.07%, 10.69%-53.57% | 34.48%, 10.81%-50.04% | 5.4%, 0%-4.17% | 5.37%, 0%-3.83% | 7.54%, 0%-3.54% | 4.43%, 0%-3.32% |
| LCR length (bp) (mean, IQR) | 68.79, 17-75 | 65.75, 17-70 | 55.08, 18-63 | 80.18, 15-72 | 73.61, 14-66 | 63.81, 11-57 | 77.55, 15-67 |
| Coverage score component (mean, IQR) | 0.571, 0.413-0.747 | 0.577, 0.425-0.75 | 0.586, 0.442-0.748 | 0.88, 0.839-1 | 0.883, 0.846-1 | 0.866, 0.851-1 | 0.895, 0.855-1 |
| % of accurate bases (bases with accuracy >= 0.95) per transcript (mean, IQR) | 97%, 95.85%-98.62% | 94.57%, 92.44%-97.1% | 89.73%, 85.78%-94.1% | 96.61%, 95.63%-98.09% | 93.64%, 91.84%-95.91% | 86.5%, 83.65%-89.57% | 97.23%, 96.48%-98.55% |
| N, % bases with accuracy >= 0.2 | 33313030, 99.92% | 31601721, 99.86% | 26925680, 99.71% | 44260356, 99.97% | 43518057, 99.95% | 41528758, 99.91% | 44887538, 99.97% |
| N, % bases with accuracy >= 0.4 | 33301040, 99.89% | 31577602, 99.78% | 26878119, 99.54% | 44254180, 99.95% | 43509893, 99.93% | 41514245, 99.87% | 44881465, 99.95% |
| N, % bases with accuracy >= 0.6 | 33253513, 99.74% | 31503527, 99.55% | 26768557, 99.13% | 44225909, 99.89% | 43473900, 99.85% | 41464738, 99.75% | 44854147, 99.89% |
| N, % bases with accuracy >= 0.8 | 33103327, 99.29% | 31281236, 98.84% | 26457510, 97.98% | 44120949, 99.65% | 43341481, 99.54% | 41279991, 99.31% | 44754124, 99.67% |
| N, % bases with accuracy >= 0.85 | 32928658, 98.77% | 30989264, 97.92% | 26025324, 96.38% | 44025332, 99.44% | 43196810, 99.21% | 41034421, 98.72% | 44668563, 99.48% |
| N, % bases with accuracy >= 0.9 | 32660971, 97.97% | 30512541, 96.41% | 25246304, 93.5% | 43846171, 99.03% | 42885186, 98.5% | 40389557, 97.17% | 44515186, 99.14% |
| N, % bases with accuracy >= 0.95 | 32023143, 96.05% | 29335708, 92.7% | 23195638, 85.9% | 42993455, 97.11% | 41164374, 94.54% | 36555969, 87.95% | 43810794, 97.57% |
| N, % bases with accuracy >= 0.99 | 31361027, 94.07% | 28186993, 89.07% | 21426951, 79.35% | 37595926, 84.91% | 31577993, 72.53% | 22265764, 53.57% | 37392839, 83.27% |
| N, % bases with accuracy >= 1 | 31347635, 94.03% | 28174215, 89.03% | 21420763, 79.33% | 36213332, 81.79% | 30224390, 69.42% | 21585912, 51.93% | 34989397, 77.92% |
| N, % assembly bases in LAR | 1002861, 3.01% | 2441506, 7.71% | 7172715, 26.56% | 988578, 2.23% | 2487513, 5.71% | 15740460, 37.87% | 961665, 2.14% |
| % of bases in LAR per transcript (mean, IQR) | 2.88%, 1.06%-3.55% | 6.9%, 3.88%-8.92% | 19.47%, 11.92%-26.44% | 2.54%, 0.59%-2.91% | 6.53%, 3.96%-7.59% | 36.09%, 31.7%-41.24% | 2.43%, 0.42%-2.79% |
| LAR length (bp) (mean, IQR) | 4, 1-4 | 4.49, 1-5 | 7.42, 1-10 | 6.89, 1-6 | 4.93, 1-6 | 7.63, 1-10 | 7.7, 1-7 |
| Accuracy score component (mean, IQR) | 0.923, 0.906-0.944 | 0.882, 0.862-0.903 | 0.814, 0.785-0.837 | 0.941, 0.924-0.967 | 0.902, 0.889-0.923 | 0.781, 0.771-0.793 | 0.944, 0.924-0.972 |
| Parameter | RSP_0.01_11_20 | RSP_0.02_11_20 |
|---|---|---|
| % of covered bases per transcript (mean, IQR) | 98.52%, 100%-100% | 95.9%, 100%-100% |
| N, % fully covered transcripts | 15188, 81.14% | 15317, 78.82% |
| N, % fully uncovered transcripts | 124, 0.66% | 634, 3.26% |
| Mean coverage per transcript (mean, IQR) | 42.79, 23.48-52.04 | 41.54, 22.5-51.51 |
| N, % bases with coverage >= 5 | 42223041, 93.69% | 40990764, 94.45% |
| N, % bases with coverage >= 10 | 39486167, 87.62% | 38595620, 88.93% |
| N, % bases with coverage >= 20 | 33438325, 74.2% | 32923129, 75.86% |
| N, % bases with coverage >= 40 | 19933054, 44.23% | 19625900, 45.22% |
| N, % bases with coverage >= 60 | 13545362, 30.06% | 13397911, 30.87% |
| N, % bases with coverage >= 80 | 8752561, 19.42% | 8658865, 19.95% |
| N, % bases with coverage >= 100 | 6137951, 13.62% | 6111579, 14.08% |
| Maximum uncovered region length per transcript (bp) (mean, IQR) | 23.38, 0-0 | 21.67, 0-0 |
| Mean end coverage per transcript (mean, IQR) | 9.65, 3.26-13.46 | 9.39, 3.43-13.1 |
| N, % assembly bases in LCR | 2152479, 4.78% | 1816114, 4.18% |
| % of bases in LCR per transcript (mean, IQR) | 4.74%, 0%-3.05% | 7.76%, 0%-2.94% |
| LCR length (bp) (mean, IQR) | 74.09, 13-64 | 65.02, 11-58 |
| Coverage score component (mean, IQR) | 0.895, 0.862-1 | 0.871, 0.864-1 |
| % of accurate bases (bases with accuracy >= 0.95) per transcript (mean, IQR) | 94.7%, 93.38%-96.72% | 87.94%, 85.47%-91.02% |
| N, % bases with accuracy >= 0.2 | 44403219, 99.95% | 42801759, 99.92% |
| N, % bases with accuracy >= 0.4 | 44394952, 99.93% | 42788744, 99.89% |
| N, % bases with accuracy >= 0.6 | 44359662, 99.85% | 42742607, 99.78% |
| N, % bases with accuracy >= 0.8 | 44234061, 99.57% | 42573551, 99.39% |
| N, % bases with accuracy >= 0.85 | 44108666, 99.29% | 42366969, 98.9% |
| N, % bases with accuracy >= 0.9 | 43851329, 98.71% | 41830500, 97.65% |
| N, % bases with accuracy >= 0.95 | 42372204, 95.38% | 38227764, 89.24% |
| N, % bases with accuracy >= 0.99 | 30710976, 69.13% | 20731797, 48.4% |
| N, % bases with accuracy >= 1 | 28447188, 64.03% | 19674527, 45.93% |
| N, % assembly bases in LAR | 2304263, 5.19% | 16911438, 39.48% |
| % of bases in LAR per transcript (mean, IQR) | 5.91%, 3.27%-6.92% | 38.22%, 34.13%-43.07% |
| LAR length (bp) (mean, IQR) | 5.06, 1-6 | 7.56, 1-10 |
| Accuracy score component (mean, IQR) | 0.908, 0.893-0.93 | 0.778, 0.768-0.79 |
IQR = interquartile range, LCR = low-coverage region, LAR = low-accuracy region
Figure 2. Per-base coverage category distribution.
Figure 3. Proportion of covered bases per transcript
category distribution.
Figure 4. Mean transcript coverage category
distribution.
Figure 5. Positional relative coverage distribution.
Figure 6. Maximum uncovered region length per
transcript distribution.
Figure 7. Mean transcript end coverage per transcript
distribution.
Figure 8. Proportion of bases in low-coverage regions
per transcript category distribution.
Figure 9. Low-coverage region length distribution.
Figure 10. Coverage score component distribution.
Figure 11. Per-base accuracy category distribution.
Figure 12. Proportion of accurate bases per transcript
category distribution.
Figure 13. Positional accuracy distribution.
Figure 14. Proportion of bases in low-accuracy regions
per transcript category distribution.
Figure 15. Low-accuracy region length distribution.
Figure 16. Accuracy score component distribution.
Table 4. Local fidelity and integrity statistics.
| Parameter | RSP_0.005_1_4 | RSP_0.01_1_4 | RSP_0.02_1_4 | RSP_0.005_5_10 | RSP_0.01_5_10 | RSP_0.02_5_10 | RSP_0.005_11_20 |
|---|---|---|---|---|---|---|---|
| N, % reads with pair not mapped to the assembly | 44671, 1.23% | 66086, 1.85% | 117364, 3.5% | 41295, 0.22% | 51628, 0.28% | 96421, 0.53% | 51420, 0.21% |
| N, % reads with pair not mapped to the assembly on transcript ends | 16728, 10.02% | 26399, 13.32% | 52156, 19.52% | 8223, 2.28% | 9713, 2.63% | 16557, 4.28% | 11085, 2.43% |
| % of reads with pair not mapped to the assembly on transcript ends per transcript (mean, IQR) | 11.56%, 0%-20% | 15.34%, 0%-25% | 22.31%, 0%-33.33% | 2.5%, 0%-0% | 3.51%, 0%-0% | 6.09%, 0%-7.69% | 2.31%, 0%-0% |
| N, % reads with pair mapped in an unexpected orientation | 4, 0% | 14, 0% | 0, 0% | 642, 0% | 2, 0% | 542, 0% | 80, 0% |
| N, % reads with pair mapped too far apart | 6080, 0.17% | 8986, 0.25% | 29414, 0.88% | 21110, 0.11% | 21000, 0.11% | 22020, 0.12% | 27712, 0.12% |
| N, % improperly paired reads within a transcript | 50755, 1.39% | 75086, 2.1% | 146778, 4.38% | 63047, 0.34% | 72630, 0.39% | 118983, 0.65% | 79212, 0.33% |
| % of improperly paired reads within a transcript per transcript (mean, IQR) | 7.22%, 0%-9.09% | 10.55%, 0.27%-14.29% | 17.62%, 3.43%-25% | 0.44%, 0%-0.23% | 0.63%, 0%-0.38% | 1.46%, 0%-0.98% | 0.41%, 0%-0.19% |
| Local fidelity score component (mean, IQR) | 0.82, 0.698-1 | 0.758, 0.622-0.948 | 0.647, 0.5-0.817 | 0.969, 0.952-1 | 0.958, 0.938-1 | 0.923, 0.901-1 | 0.97, 0.956-1 |
| N, % reads with pair mapped to another transcript | 92682, 2.54% | 105812, 2.95% | 137456, 4.1% | 288946, 1.56% | 287574, 1.56% | 275434, 1.51% | 379216, 1.58% |
| % of reads with pair mapped to another transcript per transcript (mean, IQR) | 14.4%, 0%-22.22% | 15.73%, 0%-25% | 17.42%, 0%-26.67% | 3.26%, 0%-2.69% | 3.44%, 0%-2.74% | 4.9%, 0%-2.92% | 3.28%, 0%-2.82% |
| N, % fragmented transcripts | 571, 2.06% | 818, 2.67% | 1499, 4.09% | 727, 3.91% | 704, 3.77% | 707, 3.68% | 808, 4.33% |
| N, % reads representing bridging events on transcript ends | 9074, 5.44% | 12520, 6.32% | 20270, 7.58% | 6614, 1.83% | 6212, 1.68% | 6478, 1.68% | 8486, 1.86% |
| % of reads representing bridging events on transcript ends per transcript (mean, IQR) | 6.36%, 0%-0% | 7.19%, 0%-12.5% | 8.24%, 0%-14.29% | 1.88%, 0%-0% | 1.76%, 0%-0% | 1.83%, 0%-0% | 1.81%, 0%-0% |
| Integrity score component (mean, IQR) | 0.714, 0.493-1 | 0.685, 0.45-1 | 0.646, 0.408-1 | 0.92, 0.891-1 | 0.917, 0.89-1 | 0.898, 0.885-1 | 0.919, 0.888-1 |
| Parameter | RSP_0.01_11_20 | RSP_0.02_11_20 |
|---|---|---|
| N, % reads with pair not mapped to the assembly | 60936, 0.25% | 110944, 0.47% |
| N, % reads with pair not mapped to the assembly on transcript ends | 10830, 2.33% | 17004, 3.54% |
| % of reads with pair not mapped to the assembly on transcript ends per transcript (mean, IQR) | 2.97%, 0%-0% | 4.97%, 0%-5.26% |
| N, % reads with pair mapped in an unexpected orientation | 48, 0% | 76, 0% |
| N, % reads with pair mapped too far apart | 27256, 0.11% | 27666, 0.12% |
| N, % improperly paired reads within a transcript | 88240, 0.37% | 138686, 0.58% |
| % of improperly paired reads within a transcript per transcript (mean, IQR) | 0.51%, 0%-0.32% | 1.08%, 0%-0.75% |
| Local fidelity score component (mean, IQR) | 0.962, 0.944-1 | 0.934, 0.914-1 |
| N, % reads with pair mapped to another transcript | 378108, 1.57% | 367392, 1.54% |
| % of reads with pair mapped to another transcript per transcript (mean, IQR) | 3.51%, 0%-2.78% | 4.66%, 0%-3.01% |
| N, % fragmented transcripts | 802, 4.28% | 806, 4.15% |
| N, % reads representing bridging events on transcript ends | 8146, 1.75% | 8818, 1.83% |
| % of reads representing bridging events on transcript ends per transcript (mean, IQR) | 1.79%, 0%-0% | 1.84%, 0%-0% |
| Integrity score component (mean, IQR) | 0.916, 0.889-1 | 0.902, 0.883-1 |
IQR = interquartile range
Figure 17. Per-transcript proportion of improperly
paired reads within a transcript category distribution.
Figure 18. Local fidelity score component distribution.
Figure 19. Per-transcript proportion of reads with pair
mapped to another transcript category distribution.
Figure 20. Integrity score component distribution.